Constructing level-2 phylogenetic networks from triplets

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):667-81. doi: 10.1109/TCBB.2009.22.

Abstract

Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bayes Theorem
  • Biological Evolution
  • Computational Biology / methods*
  • Computer Simulation
  • Data Interpretation, Statistical
  • Likelihood Functions
  • Models, Statistical
  • Phylogeny
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software
  • Time Factors